Explosion of the bombs in Hiroshima and Nagasaki corresponds to the only historical moment when atomic bombs were used against civilians. This event triggered countless investigations into the effects and dosimetry of ionizing radiation. However, none of the investigations has used the victims’ bones as dosimeter. Here, we assess samples of bones obtained from fatal victims of the explosion by Electron Spin Resonance (ESR). In 1973, one of the authors of the present study (SM) traveled to Japan and conducted a preliminary experiment on the victims’ bone samples. The idea was to use the paramagnetism induced in bone after irradiation to measure the radiation dose. Technological advances involved in the construction of spectrometers, better knowledge of the paramagnetic center, and improvement in signal processing techniques have allowed us to resume the investigation. We obtained a reconstructed dose of 9.46 ± 3.4 Gy from the jawbone, which was compatible with the dose distribution in different locations as measured in non-biological materials such as wall bricks and roof tiles.

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes.How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components.This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.

Keywords Evolutionary biology Interactions Theoretical biology Tree of Life Web of Life

More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.

There have been periodic claims that evolutionary biology needs urgent reform, and this article tries to account for the volume and persistence of this discontent. It is argued that a few inescapable properties of the field make it prone to criticisms of predictable kinds, whether or not the criticisms have any merit. For example, the variety of living things and the complexity of evolution make it easy to generate data that seem revolutionary (e.g. exceptions to well-established generalizations, or neglected factors in evolution), and lead to disappointment with existing explanatory frameworks (with their high levels of abstraction, and limited predictive power). It is then argued that special discontent stems from misunderstandings and dislike of one well-known but atypical research programme: the study of adaptive function, in the tradition of behavioural ecology. To achieve its goals, this research needs distinct tools, often including imaginary agency, and a partial description of the evolutionary process. This invites mistaken charges of narrowness and oversimplification (which come, not least, from researchers in other subfields), and these chime with anxieties about human agency and overall purpose. The article ends by discussing several ways in which calls to reform evolutionary biology actively hinder progress in the field.

This review aims to highlight the key areas in which changes to the epigenome have played an important role in the evolution and development of our species. Firstly, there will be a brief introduction into the topic of epigenetics to outline the current understanding of the subject and inform the reader of the basic mechanisms and functions of the epigenome. This will lead on to more focussed detail on the role played by epigenetic changes in the rapid evolution of our species and emergence from our ancestor species, as well as the Human Accelerated Regions that played a role in this. The discussion highlights how epigenetics has helped and hindered our species’ development via changes to the epigenome in more modern times, discussing case examples of documented instances where it is shown that epigenetics has played a role in the evolution of humanity.

Robustness, and the ability to function and thrive amid changing and unfavorable environments, is a fundamental requirement for living systems. Until now it has been an open question how large and complex biological networks can exhibit robust behaviors, such as perfect adaptation to a variable stimulus, since complexity is generally associated with fragility. Here we report that all networks that exhibit robust perfect adaptation (RPA) to a persistent change in stimulus are decomposable into well-defined modules, of which there exist two distinct classes. These two modular classes represent a topological basis for all RPA-capable networks, and generate the full set of topological realizations of the internal model principle for RPA in complex, self-organizing, evolvable bionetworks. This unexpected result supports the notion that evolutionary processes are empowered by simple and scalable modular design principles that promote robust performance no matter how large or complex the underlying networks become.

Acknowledgements

This study was partially supported by NIH grants R33CA206937 and R01AR068436.

Author information

Affiliations

School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD, 4000, Australia

Have you read a paper and thought: “How could peer reviews support the publication of such a paper?” I have. More than once. Other times, I have read fascinating papers outside of my field and wondered what the concerns of the experts who peer reviewed the study were. What important caveats am I missing?

Sometimes, I am lucky and find the answers to such questions: A few publications, including those from EMBO Press and eLife, publish the peer reviews alongside the papers. Reading such peer reviews has provided an additional dimension of appreciating and understanding the experiments and the findings, especially when I am not very familiar with the topic. But for most other journals I cannot access the peer reviews that supported a paper’s publication because most journals hide them.

How do we know that a journal conducts peer review? For most journals, the evidence is limited to our anecdotal experiences with the manuscripts that we review ourselves or that we and our friends have submitted. For me this evidence is mixed. I know of manuscripts that have been thoughtfully reviewed and manuscripts that have undergone very expedited peer review or no peer review at all before appearing in the most prestigious journals. This anecdotal evidence is rather weak. If you ask me to substantiate it, I have to refer you to a friend who may or may not be willing to tell you that his or her paper was barely peer reviewed. It is a huge problem that the evidence for such a centrally important process is hidden from public view.

Euarthropoda is one of the best-preserved fossil animal groups and has been the most diverse animal phylum for over 500 million years. Fossil Konservat-Lagerstätten, such as Burgess Shale-type deposits (BSTs), show the evolution of the euarthropod stem lineage during the Cambrian from 518 million years ago (Ma). The stem lineage includes nonbiomineralized groups, such as Radiodonta (e.g., Anomalocaris) that provide insight into the step-by-step construction of euarthropod morphology, including the exoskeleton, biramous limbs, segmentation, and cephalic structures. Trilobites are crown group euarthropods that appear in the fossil record at 521 Ma, before the stem lineage fossils, implying a ghost lineage that needs to be constrained. These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana, Rusophycus) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma. While each of the major types of fossil evidence (BSTs, trace fossils, and biomineralized preservation) have their limitations and are incomplete in different ways, when taken together they allow a coherent picture to emerge of the origin and subsequent radiation of total group Euarthropoda during the Cambrian.

We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion – life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.

The usual theory of inflation breaks down in eternal inflation. We derive a dual description of eternal inflation in terms of a deformed Euclidean CFT located at the threshold of eternal inflation. The partition function gives the amplitude of different geometries of the threshold surface in the no-boundary state. Its local and global behavior in dual toy models shows that the amplitude is low for surfaces which are not nearly conformal to the round three-sphere and essentially zero for surfaces with negative curvature. Based on this we conjecture that the exit from eternal inflation does not produce an infinite fractal-like multiverse, but is finite and reasonably smooth.

First Detailed Anatomical Study of Bonobos Reveals Intra-Specific Variations and Exposes Just-So Stories of Human Evolution, Bipedalism, and Tool Use

Rui Diogo*

Department of Anatomy, Howard University, Washington, DC, United States

Figure 1. Differences between head muscles of common chimps, bonobos, and humans, based and modified from Diogo et al. (2017b).

Just-so stories are prominent in human evolution literature because of our tendency to create simple progressionist narratives about our “special” place in nature, despite the fact that these stories are almost exclusively based on hard tissue data. How can we be so certain about the evolution of human facial communication, bipedalism, tool use, or speech without detailed knowledge of the internal anatomy of for instance, one of the two extant species more closely related to us, the bonobos? Here I show how many of these stories now become obsolete, after such a comprehensive knowledge on the anatomy of bonobos and other primates is finally put together. Each and every muscle that has been long accepted to be “uniquely human” and to provide “crucial singular functional adaptations” for our bipedalism, tool use and/or vocal/facial communication, is actually present as an intra-specific variant or even as normal phenotype in bonobos and/or other apes.

Just-so stories (Smith, 2016) are frequent in the literature about human evolution because of our tendency to build simple progressionist narratives about our “special” evolutionary history and place in nature (Gould, 1993, 2002). This is particularly striking because these stories are in reality almost exclusively based on hard tissue data. In fact, descriptions of the soft tissues of apes have been relatively scarce and mainly referred to just a few muscles of the head or limbs of a single taxon, in most cases (e.g., Tyson, 1699; Bischoff, 1880; Raven, 1950; Swindler and Wood, 1973; Diogo and Wood, 2011, 2012; Persaud and Loukas, 2014). For instance, the only study that specifically focused on the musculature of bonobos (Pan paniscus) was that of Miller (1952), which was based on dissections of a single adult and did not provide information for numerous head and limb muscles (Diogo and Wood, 2011, 2012). Strikingly, despite this scarcity of information, biologists and anthropologists have displayed a remarkable confidence in their stories about the origin and evolution of human soft tissues, including their phylogenetic distribution and “singular functional adaptations.”

To illustrate this fact, in this short paper I will refer here briefly to seven muscles that have long been generally seen as “unique human features” and linked with specific adaptations for our bipedalism, tool use, and vocal or facial communication. Firstly, the facial expression muscle risorius (Figure 1) has been generally accepted as a unique feature crucial for the evolution of our “gracile” smile and “specially sophisticated” facial communication abilities (Huber, 1931). In a very influential paper, Susman et al. argued—although (fortunately) not as confidently as the assertions done by some of the other authors cited here—that the hand muscle adductor pollicis accessorius (Figure 2; “Henle” or “interosseous volaris primus” muscle: Bello-Hellegouarch et al., 2013) is a unique feature likely related to our increased ability to manufacture and/or use tools (Susman et al., 1999). Similarly, the foot muscle adductor hallucis accessorius—which topologically corresponds to the adductor pollicis accessorius of the hand—is also often considered to be uniquely found in our bipedal species, being at least consistently present at early stages of our ontogenetic development (Cihak, 1972). The foot muscle fibularis tertius (Figure 3) is, according to Lewis' (1989) highly influential monograph on the evolution of our limbs, a unique feature most likely associated with our bipedal evolution (Lewis, 1989). The flexor pollicis longus and extensor pollicis brevis (Figure 2) are forearm muscles that insert onto the thumb and that are generally considered to be unique adaptations for human tool manufacture and use (Lewis, 1989). For instance, it has been experimentally shown that the recruitment to these two muscles allows human subjects to maintain the metacarpophalangeal joint in extension while flexing the distal phalanx of the thumb, i.e., two primary movements usually done when we grab/manipulate objects (Marzke et al., 1998; Williams et al., 2012). Lastly, the laryngeal muscle arytenoideus obliquus has long been considered to be a unique feature of humans—which also have an arytenoideus transversus, in contrast to the single arytenoideus muscle said to occur in all other primates—associated to our enhanced vocal communication (reviewed in Diogo and Wood, 2012).

The “tree of life” has become a metaphor for the interconnectivity and breadth of all life on Earth. It also has come to symbolize the broad investigation of biodiversity, including both the reconstruction of phylogeny and the numerous downstream analyses that are possible with a firm phylogenetic underpinning. Only a few decades ago, the construction of large phylogenetic trees of hundreds of taxa (or more) was considered an impossible task due to the immense computational challenges posed by analyses of large data sets. And no wonder—the number of possible trees that can describe the relationships of just 200 species exceeds the number of atoms in the universe (Hillis, 1996). As a result, building the tree of all named life, including the green plant branch (Viridiplantae)—a major clade with perhaps 500,000 species—has long been considered a grand challenge in biology. However, a perfect storm of algorithm development, increases in computational power, and DNA sequencing improvements over the last decade has not only made the construction of large trees more feasible, but also allowed us to attain some far‐reaching goals—a noteworthy example being the recent publication of a first draft tree of all life (Hinchcliff et al., 2015).

In plant biology, the frequent reconstruction of large phylogenetic trees has had an immense impact on the field. Large trees have helped to resolve deep‐level relationships and resulted in the revision of classifications, including some of the most profound changes in our view of plant relationships over the past 200 years (e.g., reviewed in part by Gitzendanner et al., 2018, in this issue). Large trees have also ushered in a renaissance in the study of conservation, ecology, methods development, crop improvement, genome evolution, and much more. Building the plant tree of life has come to represent the biodiversity equivalent of the human genome project, with numerous and often unanticipated downstream outcomes.

Accompanying these exciting advances are equally significant challenges that remain for the construction of a better and more complete picture of the evolution of plant lineages. In addition to the computational challenges of larger data sets, these include conceptual and methodological barriers. For example, where it was once thought that simply increasing DNA sequence data would increase resolution of relationships, we now understand that increasing data leads to increasing analytical complexity. Furthermore, this complexity is not due solely to limitations in computational power and methodology, but in part reflects the underlying complexity of the evolutionary process and its impact on genomes. Nevertheless, current conceptual and computational limitations present fantastic opportunities for transformative developments in our understanding of plant evolution. In this special issue, we explore many of the uses and challenges of big trees and big data in plant biology. Diverse papers provide overviews of the current status of the green plant tree of life and describe some of the myriad applications of the knowledge of phylogenetic relationships as well as some of the challenges inherent in handling plant phylogenomic data.

The field of synthetic molecular machines has quickly evolved in recent years, growing from a fundamental curiosity to a highly active field of chemistry. Many different applications are being explored in areas such as catalysis, self-assembled and nanostructured materials, and molecular electronics. Rotary molecular motors hold great promise for achieving dynamic control of molecular functions as well as for powering nanoscale devices. However, for these motors to reach their full potential, many challenges still need to be addressed. In this paper we focus on the design principles of rotary motors featuring a double-bond axle and discuss the major challenges that are ahead of us. Although great progress has been made, further design improvements, for example in terms of efficiency, energy input, and environmental adaptability, will be crucial to fully exploit the opportunities that these rotary motors offer.

The bacterial flagellum is a supramolecular motility machine. Flagellar assembly begins with the basal body, followed by the hook and finally the filament. A carboxyl-terminal cytoplasmic domain of FlhA (FlhAC) forms a nonameric ring structure in the flagellar type III protein export apparatus and coordinates flagellar protein export with assembly. However, the mechanism of this process remains unknown. We report that a flexible linker of FlhAC (FlhAL) is required not only for FlhAC ring formation but also for substrate specificity switching of the protein export apparatus from the hook protein to the filament protein upon completion of the hook structure. FlhAL was required for cooperative ring formation of FlhAC. Alanine substitutions of residues involved in FlhAC ring formation interfered with the substrate specificity switching, thereby inhibiting filament assembly at the hook tip. These observations lead us to propose a mechanistic model for export switching involving structural remodeling of FlhAC.

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

High‐throughput ‐omics techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision‐making is inherently a unicellular process to which “bulk” ‐omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single‐cell methods bridge this gap, allowing high‐throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single‐cell gene expression data and highlight areas of developmental biology where single‐cell techniques have made important contributions. These include understanding of cell‐to‐cell heterogeneity, the tracing of differentiation pathways, quantification of gene expression from specific alleles, and the future directions of cell lineage tracing and spatial gene expression analysis.

A convenient and inherently more secure communication channel for encoding messages via specifically designed molecular keys is introduced by combining advanced encryption standard cryptography with molecular steganography. The necessary molecular keys require large structural diversity, thus suggesting the application of multicomponent reactions. Herein, the Ugi four-component reaction of perfluorinated acids is utilized to establish an exemplary database consisting of 130 commercially available components. Considering all permutations, this combinatorial approach can unambiguously provide 500,000 molecular keys in only one synthetic procedure per key. The molecular keys are transferred nondigitally and concealed by either adsorption onto paper, coffee, tea or sugar as well as by dissolution in a perfume or in blood. Re-isolation and purification from these disguises is simplified by the perfluorinated sidechains of the molecular keys. High resolution tandem mass spectrometry can unequivocally determine the molecular structure and thus the identity of the key for a subsequent decryption of an encoded message.

Acknowledgements

We thank PD Dr. Weiss, T. Neck, and Dr. N. Boukis for the discussions and comments on early versions of this manuscript. A.B. is grateful for the Chemie Fonds fellowship from the VCI. This work was financially supported in part by SFB 1176 (Projects A3 and Q5). We thank Prof. Podlech for sharing lab space with us. We acknowledge support by Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of Karlsruhe Institute of Technology.

A.B. and M.M. conceived and designed the project. A.B. designed the experiments with input from M.M. K.R. programed the analysis script. M.F. synthesized the molecular keys under the supervision of A.B. D.H. optimized the cryptography integration and programed the molecular encryption script. A.B. analyzed data, prepared the figures and wrote the paper, with feedback from all the authors.